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Difference between revisions of "Coexpression cluster:C383"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0000468!2.74e-18!659;UBERON:0000475!2.92e-17!365;UBERON:0000467!2.39e-13!625;UBERON:0000480!4.86e-13!626;UBERON:0000481!5.55e-12!347;UBERON:0000119!1.61e-10!312;UBERON:0000922!3.02e-10!612;UBERON:0004121!3.74e-10!169;UBERON:0000483!4.21e-10!309;UBERON:0000924!4.28e-10!173;UBERON:0006601!4.28e-10!173;UBERON:0000062!5.02e-10!511;UBERON:0000477!7.04e-10!286;UBERON:0002050!1.00e-09!605;UBERON:0005423!1.00e-09!605;UBERON:0000923!1.59e-09!604;UBERON:0005291!1.59e-09!604;UBERON:0006598!1.59e-09!604;UBERON:0002532!1.59e-09!604;UBERON:0000064!1.77e-09!219;UBERON:0000033!4.76e-09!123;UBERON:0004111!5.96e-09!241;UBERON:0000153!2.38e-08!129;UBERON:0007811!2.38e-08!129;UBERON:0005631!9.30e-08!14;UBERON:0000158!9.30e-08!14;UBERON:0002100!1.13e-07!216;UBERON:0004923!1.35e-07!57;UBERON:0001444!9.26e-07!48
 
|ontology_enrichment_uberon=UBERON:0000468!2.74e-18!659;UBERON:0000475!2.92e-17!365;UBERON:0000467!2.39e-13!625;UBERON:0000480!4.86e-13!626;UBERON:0000481!5.55e-12!347;UBERON:0000119!1.61e-10!312;UBERON:0000922!3.02e-10!612;UBERON:0004121!3.74e-10!169;UBERON:0000483!4.21e-10!309;UBERON:0000924!4.28e-10!173;UBERON:0006601!4.28e-10!173;UBERON:0000062!5.02e-10!511;UBERON:0000477!7.04e-10!286;UBERON:0002050!1.00e-09!605;UBERON:0005423!1.00e-09!605;UBERON:0000923!1.59e-09!604;UBERON:0005291!1.59e-09!604;UBERON:0006598!1.59e-09!604;UBERON:0002532!1.59e-09!604;UBERON:0000064!1.77e-09!219;UBERON:0000033!4.76e-09!123;UBERON:0004111!5.96e-09!241;UBERON:0000153!2.38e-08!129;UBERON:0007811!2.38e-08!129;UBERON:0005631!9.30e-08!14;UBERON:0000158!9.30e-08!14;UBERON:0002100!1.13e-07!216;UBERON:0004923!1.35e-07!57;UBERON:0001444!9.26e-07!48
 +
|tfbs_overrepresentation=0.773893,0.431239,0.629215,0.366388,0.875059,0.00536527,0.336542,0.875099,0.266916,0.215773,0.753752,0.687931,0.858092,0.357772,0.777393,0.449204,0.757885,0.618915,0.397575,0.656063,0.85787,0.734853,0.549909,0.605686,0.327196,0.661039,0.888407,0.588371,0.765062,0.599427,0.88242,0.677024,0.000719122,0.640362,0.474034,0.561199,0.0515186,0.336289,0.697851,0.474975,0.61207,0.207515,0.755392,0.850143,0.69966,0.291451,0.303538,0.557497,0.667498,0.700565,0.790211,0.405414,0.492869,0.597879,0.612225,0.306233,0.653891,0.385891,0.532911,0.647016,0.243312,0.779188,0.658018,0.521554,0.407696,0.383403,0.769618,0.438751,0.568305,0.818409,0.648414,0.480065,0.581196,0.694733,0.0676422,0.148834,0.612125,0.340975,0.298337,0.0656805,0.608646,0.909467,0.0629902,0.31508,0.959806,0.752768,0.462435,0.887932,0.992461,0.453827,0.566912,0.377921,0.60765,0.364263,0.565282,0.680349,0.575402,0.789191,0.596846,0.799391,0.424532,0.951061,0.760221,0.297092,0.900547,0.322968,0.476467,0.978747,0.766262,0.946533,0.84769,0.2759,0.779515,0.153412,0.630659,0.274187,0.174515,0.419781,0.407153,0.197425,0.81771,0.895217,0.755617,0.567027,0.635036,0.273969,0.588228,0.129862,0.560699,0.741496,0.436342,0.516146,0.422996,0.193564,0.714853,0.656219,0.465235,0.412164,0.269175,0.0363132,0.193486,0.720326,0.0649963,0.794629,0.848295,0.488535,0.621358,0.560103,0.309765,0.00779664,0.87634,0.764882,0.118592,0.222331,0.334607,0.688749,0.515779,0.911065,0.390697,0.273994,0.910346,0.607247,0.68575,0.439692,0.00365843,0.67783,0.317039,0.719615,0.319175,0.969548,0.842553,0.749182,0.524982,0.405155,0.540466,0.58565,0.756175,0.846324,0.54737,0.287271,0.801002,0.704588,0.228456,0.682185,0.510701,0.692995,0.848439,0.317991,0.553978,0.831229,0.652767,0.305908,0.706034,0.696966,0.672314,0.362388,0.532574,0.115472,0.479918,0.661835,0.582335,0.440916,0.253451,0.442057,0.745701,0.939365,0.798327,0.785013,0.884265,0.114158,0.354815,0.642513,0.700415,0.673102,0.462978,0.250313,0.812524,0.62959,0.455174,0.637389,0.760367,0.987076,0.469763,0.487482,0.511367,0.717336,0.0140659,0.567867,0.441222,0.438122,0.00713158,0.663404,0.328952,0.524229,0.609823,0.598704,0.36335,0.942117,0.811053,0.895335,0.290987,0.981798,0.074293,0.554986,0.684555,0.746762,0.54777,0.66877,0.987144,0.687027,0.0811414,0.852094,0.128357,0.618233,0.618475,0.482683,0.653117,0.621512,0.489898,0.0712985,0.449322,0.108164,0.810788,0.721788,0.279503,0.545732,0.546175,0.594015,0.690485,0.167303,0.807429,0.456784,0.935727,0.801114,0.570583,0.303736,0.727916,0.826963,0.615887,0.0340836,0.984362,0.369452,0.553022,0.0992859,0.977932,0.982445,0.940982,0.0257473,0.810903,0.670352,0.986719,0.976425,0.332159,0.97605,0.999208,0.285372,0.948304,0.960241,0.118962,0.850257,0.820803,0.0508704,0.855592,0.411369,0.846146,0.0782115,0.662948,0.322502,0.899641,0.267287,0.987911,0.830665,0.996558,0.403321,0.156104,0.986752,0.562017,0.738885,0.756658,0.358374,0.965015,0.860465,0.97147,0.905672,0.478156,0.162389,0.955598,0.46933,0.90291,0.960008,0.321449,0.113558,0.136844,0.960597,0.08706,0.454601,0.932052,0.553154,0.974917,0.847291,0.472531,0.924896,0.824663,0.950509,0.919394,0.852933,0.560241,0.926142,0.341544,0.137556,0.33114,0.801086,0.912371,0.930613,0.954338,0.845882,0.810509,0.476789,0.50758,0.851465,0.924485,0.997263,0.961393,0.872761,0.997985,0.128281,0.940276,0.0562305,0.0840449,0.14256,0.66897,0.350008,0.515747,0.697462,0.925089,0.835235,0.988818,0.410485,0.902776,0.402539,0.958668,0.975217,0.999743,0.585871,0.969277,0.15787,0.434559,0.531853,0.871915,0.213131,0.664393,0.99395,0.997869,0.143393,0.0837604,0.462803,0.893398,0.767767,0.76961,0.989381,0.815392,0.319396,0.978513,0.933652,0.786972,0.359247,0.747472,0.308213,0.741094,0.620427,0.127234,0.961044,0.380921,0.103619,0.967182,0.853873,0.0961771,0.957816,0.968209,0.818929,0.941713,0.784065,0.908749,0.863125,0.993507,0.792293,0.930283,0.838972,0.884161,0.969363,0.764933,0.621013,0.560352,0.345379,0.621977,0.954249,0.759919,0.00569161,0.967075,0.802702,0.721628,0.631093,0.447626,0.583373,0.581634,0.436255,0.99904,0.950265,0.0500644,0.929705,0.764656,0.716976,0.992085,0.73712,0.708557,0.0689895,0.490844,0.41418,0.864135,0.53137,0.424999,0.179871,0.905546,0.166188,0.995746,0.0235976,0.14058,0.669756,0.827214,0.339971,0.965732,0.716933,0.741271,0.651841,0.949203,0.454074,0.938023,0.155219,0.0224415,0.95327,0.990142,0.358692,0.517427,0.678847,0.643265,0.585117,0.571049,0.80317,0.652642,0.342064,0.035729,0.708085,0.72493,0.889687,0.144534,0.981102,0.38029,0.554096,0.474928,0.846969,0.667479,0.900897,0.977109,0.868843,0.733776,0.134267,0.369264,0.875361,0.715025,0.364565,0.83542,0.56722,0.0977991,0.575178,0.607041,0.10026,0.904451,0.652395,0.950441,0.044033,0.831509,0.758245,0.891275,0.24795,0.73191,0.346289,0.394664,0.887711,0.788155,0.5398,0.615826,0.803865,0.707879,0.222719,0.414888,0.598851,0.991359,0.748111,0.128266,0.469664,0.650454,0.674964,0.541474,0.520788,0.0263847,0.865185,0.409648,0.531244,0.417071,0.32845,0.279702,0.309307,0.935648,0.824923,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}}
 
}}

Revision as of 10:29, 8 August 2012


Full id: C383_oral_liposarcoma_small_Small_skeletal_amniotic_Astrocyte



Phase1 CAGE Peaks

Hg19::chr10:99400163..99400169,-p@chr10:99400163..99400169
-
Hg19::chr11:30496173..30496192,+p@chr11:30496173..30496192
+
Hg19::chr11:30496199..30496218,+p@chr11:30496199..30496218
+
Hg19::chr17:70680022..70680046,-p@chr17:70680022..70680046
-
Hg19::chr18:3602688..3602692,+p1@MGC11082
Hg19::chr20:23120219..23120223,-p@chr20:23120219..23120223
-
Hg19::chr2:120974061..120974068,-p3@ENST00000455707
Hg19::chr2:209003854..209003858,-p@chr2:209003854..209003858
-
Hg19::chr3:54660709..54660712,-p@chr3:54660709..54660712
-
Hg19::chr6:102844491..102844494,+p@chr6:102844491..102844494
+
Hg19::chr6:123728153..123728175,-p@chr6:123728153..123728175
-
Hg19::chr6:125186828..125186832,+p@chr6:125186828..125186832
+
Hg19::chr6:125283093..125283144,+p@chr6:125283093..125283144
+
Hg19::chr6:125283157..125283197,+p1@RNF217
Hg19::chr6:125283201..125283226,+p6@RNF217
Hg19::chr6:125283242..125283303,+p2@RNF217
Hg19::chr6:125283415..125283431,+p7@RNF217
Hg19::chr6:125283436..125283477,+p5@RNF217
Hg19::chr6:125284075..125284181,+p4@RNF217
Hg19::chr6:125284314..125284343,+p8@RNF217
Hg19::chr6:125284359..125284375,+p9@RNF217
Hg19::chr6:125284405..125284429,-p4@ENST00000439075
Hg19::chr6:125284416..125284459,+p10@RNF217
Hg19::chr6:125284525..125284534,-p8@ENST00000439075
Hg19::chr6:125284540..125284551,-p7@ENST00000439075
Hg19::chr6:125314790..125314796,+p@chr6:125314790..125314796
+
Hg19::chr6:125426966..125426967,+p@chr6:125426966..125426967
+
Hg19::chr8:101661887..101661901,-p2@SNX31


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0042787protein ubiquitination during ubiquitin-dependent protein catabolic process0.00632874131637819
GO:0016567protein ubiquitination0.0315382275599513
GO:0032446protein modification by small protein conjugation0.0315382275599513
GO:0004842ubiquitin-protein ligase activity0.0315382275599513
GO:0008639small protein conjugating enzyme activity0.0315382275599513
GO:0019787small conjugating protein ligase activity0.0315382275599513
GO:0006511ubiquitin-dependent protein catabolic process0.0315382275599513
GO:0043632modification-dependent macromolecule catabolic process0.0315382275599513
GO:0019941modification-dependent protein catabolic process0.0315382275599513
GO:0051603proteolysis involved in cellular protein catabolic process0.0315382275599513
GO:0044257cellular protein catabolic process0.0315382275599513
GO:0016881acid-amino acid ligase activity0.0315382275599513
GO:0030163protein catabolic process0.0335423289768044
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0335423289768044
GO:0043285biopolymer catabolic process0.038309980768476
GO:0044265cellular macromolecule catabolic process0.0408762233257838
GO:0006512ubiquitin cycle0.0408762233257838
GO:0009057macromolecule catabolic process0.0431020592810178
GO:0016874ligase activity0.0431020592810178



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.74e-18659
organism subdivision2.92e-17365
anatomical system2.39e-13625
anatomical group4.86e-13626
multi-tissue structure5.55e-12347
cell layer1.61e-10312
embryo3.02e-10612
ectoderm-derived structure3.74e-10169
epithelium4.21e-10309
ectoderm4.28e-10173
presumptive ectoderm4.28e-10173
organ5.02e-10511
anatomical cluster7.04e-10286
embryonic structure1.00e-09605
developing anatomical structure1.00e-09605
germ layer1.59e-09604
embryonic tissue1.59e-09604
presumptive structure1.59e-09604
epiblast (generic)1.59e-09604
organ part1.77e-09219
head4.76e-09123
anatomical conduit5.96e-09241
anterior region of body2.38e-08129
craniocervical region2.38e-08129
extraembryonic membrane9.30e-0814
membranous layer9.30e-0814
trunk1.13e-07216
organ component layer1.35e-0757
subdivision of head9.26e-0748


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.